/* * Copyright 2012 - 2018 EMBL - European Bioinformatics Institute * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this * file except in compliance with the License. You may obtain a copy of the License at * http://www.apache.org/licenses/LICENSE-2.0 * Unless required by applicable law or agreed to in writing, software distributed under the * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR * CONDITIONS OF ANY KIND, either express or implied. See the License for the * specific language governing permissions and limitations under the License. */ package net.sf.cram.cg; import htsjdk.samtools.SAMUtils; class EvidenceRecord { public String IntervalId = null; public String Chromosome = null; public String Slide = null; public String Lane = null; public String FileNumInLane = null; public String DnbOffsetInLaneFile = null; public String AlleleIndex = null; public String Side = null; public String Strand = null; public String OffsetInAllele = null; public String AlleleAlignment = null; public String OffsetInReference = null; public String ReferenceAlignment = null; public String MateOffsetInReference = null; public String MateReferenceAlignment = null; public String MappingQuality = null; public String ScoreAllele0 = null; public String ScoreAllele1 = null; public String ScoreAllele2 = null; public String Sequence = null; public String Scores = null; public int interval = 0; public int side = 0; public boolean negativeStrand = false; public int mapq = 0; public int pos = 0; public String line = null; public String name = null; public String getReadName() { return name; } public static EvidenceRecord fromString(String line) { String[] words = line.split("\t"); EvidenceRecord r = new EvidenceRecord(); r.line = line; int i = 0; r.IntervalId = words[i++]; r.Chromosome = words[i++]; r.Slide = words[i++]; r.Lane = words[i++]; r.FileNumInLane = words[i++]; r.DnbOffsetInLaneFile = words[i++]; r.AlleleIndex = words[i++]; r.Side = words[i++]; r.Strand = words[i++]; r.OffsetInAllele = words[i++]; r.AlleleAlignment = words[i++]; r.OffsetInReference = words[i++]; r.ReferenceAlignment = words[i++]; r.MateOffsetInReference = words[i++]; r.MateReferenceAlignment = words[i++]; r.MappingQuality = words[i++]; r.ScoreAllele0 = words[i++]; r.ScoreAllele1 = words[i++]; r.ScoreAllele2 = words[i++]; r.Sequence = words[i++]; r.Scores = words[i++]; r.interval = Integer.valueOf(r.IntervalId); r.negativeStrand = "+".equals(r.Strand) ? false : true; r.side = "L".equals(r.Side) ? 0 : 1; r.name = String.format("%s-%s-%s:%s", r.Slide, r.Lane, r.FileNumInLane, r.DnbOffsetInLaneFile); r.mapq = Integer.valueOf(SAMUtils.fastqToPhred(r.MappingQuality.charAt(0))); r.pos = Integer.valueOf(r.OffsetInReference); return r; } }